ProTherm: Thermodynamic Databasefor Proteins and Mutants
M. Michael Gromiha

1Jianghong An

1

Hidetoshi Kono

1

gromiha@rtc.riken.go.jp

ajh@rtc.riken.go.jp

hkono@rtc.riken.go.jp

Motohisa Oobatake

Hatsuho Uedaira

Akinori Sarai

12

oobatake@meijo-u.ac.jp

1uedaira@rtc.riken.go.jp

1sarai@rtc.riken.go.jp

1 Tsukuba Life Science Center, The Institute of Physical and Chemical Research(RIKEN), 3-1-1 Koyadai, Tsukuba, Ibaraki 305-0074, Japan
2 Faculty of Science and Technology, Meijo University, 1-501 Shiogamaguchi, Tenpakuku, Nagoya 468-8502, Japan1 Introduction

Thermodynamic data for proteins are important for understanding the mechanism of protein stability
as well as protein engineering. Recently, several mutation databases have been developed for speci cobjectives. On the other hand, there are no electronically accessible databases for thermodynamic dataon protein stability. Thus, we have developed a database, Thermodynamic Database for Proteins
and Mutants (ProTherm) [1], which includes several thermodynamic data, structural information,measuring methods, experimental conditions and literature information. This database will help tounderstand the mechanism of protein stability. A WWW interface will enable users to search thedatabase through the Internet.
2 Contents of the database

Each entry in the database is identi ed by a serial number and includes the following information:(i) Structural information: protein name, enzyme code, Protein Mutant Database (PMD) numbers,Protein Data Bank (PDB) code for wild and mutant structures, wild and mutant residue names withresidue number showing the nature of mutation, information on monomeric and oligomeric states, secondary structure, accessibility and number of transition states. (ii) Thermodynamic data obtained fromdenaturant denaturation experiments: unfolding Gibbs free energy change in the absence and presenceof denaturant (1GH2O, 1G), di erence in unfolding Gibbs free energy changes in the absence andpresence of denaturant (11GH2O, 11G), Temperature (T), midpoint of denaturant concentration(Cm) and slope of denaturation curve (m). (iii) Thermodynamic data obtained from thermal denaturation experiments: unfolding Gibbs free energy change (1G), di erence in Gibbs free energy changes(11G), transition temperature (Tm), transition temperature change (1Tm), enthalpy change (1H )and heat capacity change (1Cp ). (iv) Experimental methods and conditions: pH, measurements andmethod. (v) Functional information: enzyme activity, binding constants etc. (vi) Literature information: keywords, reference, authors and remarks.
3 Search options

A WWW interface enables users to search data based on various conditions with di erent sorting
options for outputs. (i) retrieving data for a particular protein. (ii) specifying the type of mutation as
single, double, multiple or wild type. Further, specifying any wild type residue and/or mutant residue
is possible. (iii) specifying secondary structures having mutations, helix (H), strand (S), turn (T) and330

coil (C). (iv) searching data based on solvent accessible surface area (ASA; in % or A2 ) of relevant
residue. The mutations are classi ed into buried (ASA < 20%), partially buried (20%  ASA  50%)and exposed (ASA > 50%). (v) extracting data for a particular measurement (CD, DSC, Fl etc.)
and a speci c method (Thermal, GdnHCl, Urea etc.), (vi) limiting data for a particular range of
H2O , 11GH2O , 1H , 1C and pH. (vii) extracting data with authors,T, Tm , 1Tm , 1G, 11G, 1G
ppublication year and key words. (viii) specifying output format by selecting various output items
and by sorting with publication year, wild type residue, mutant residue, residue number, secondary
structure, accessibility, pH, T, Tm, 1Tm, 1H , 1G, 11G, m, Cm, 1GH2O and 11GH2O.
4 Links to other databases

ProTherm is cross-linked with NCBI PUBMED literature database, Protein Mutant Database, Enzyme code and Protein Data Bank structural database. Moreover, all the mutation sites associatedwith each PDB structure are automatically mapped and can be directly viewed through 3DinSight
developed in our laboratory.
5 Availability

The database is freely available at the URL, http://www.rtc.riken.go.jp/protherm.html.
References[1] Gromiha, M.M., An, J., Kono, H., Oobatake, M., Uedaira, H. and Sarai, A., ProTherm: Thermodynamic database for proteins and mutants, Nucleic Acids Res., 1999 (in press).

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